Genetic Variant ENST00000562058.5:n.424-131A>C (chr16-28620264-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000562058.5(ENSG00000289755):n.424-131A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.638 in 827,720 control chromosomes in the GnomAD database, including 172,672 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as (no stars).

Frequency

Genomes: 𝑓 0.60 ( 28469 hom., cov: 31)

Exomes 𝑓: 0.65 ( 144203 hom. )

Consequence

ENSG00000289755
ENST00000562058.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.49

Publications

26 publications found

Variant links:

Genes affected

ENSG00000289755 (HGNC:):

ENSG00000289755 links:

SULT1A1 (HGNC:11453): (sulfotransferase family 1A member 1) Sulfotransferase enzymes catalyze the sulfate conjugation of many hormones, neurotransmitters, drugs, and xenobiotic compounds. These cytosolic enzymes are different in their tissue distributions and substrate specificities. The gene structure (number and length of exons) is similar among family members. This gene encodes one of two phenol sulfotransferases with thermostable enzyme activity. Multiple alternatively spliced variants that encode two isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]

SULT1A1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.01).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.915 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000562058.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank	Protein	UniProt
SULT1A1	NM_001394421.1	c.-409-131A>C	intron	N/A	NP_001381350.1	P50225-1
SULT1A1	NM_001394422.1	c.-1208-131A>C	intron	N/A	NP_001381351.1	P50225-1
SULT1A1	NM_001394423.1	c.-539-131A>C	intron	N/A	NP_001381352.1	P50225-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
ENSG00000289755	ENST00000562058.5	TSL:1	n.424-131A>C	intron	N/A
ENSG00000289755	ENST00000564818.5	TSL:1	n.123-131A>C	intron	N/A
ENSG00000289755	ENST00000563493.1	TSL:5	n.496-131A>C	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.601

AC:

91302

AN:

151824

Hom.:

28460

Cov.:

show subpopulations

Gnomad AFR

AF:

0.479

Gnomad AMI

AF:

0.811

Gnomad AMR

AF:

0.631

Gnomad ASJ

AF:

0.693

Gnomad EAS

AF:

0.937

Gnomad SAS

AF:

0.776

Gnomad FIN

AF:

0.548

Gnomad MID

AF:

0.801

Gnomad NFE

AF:

0.629

Gnomad OTH

AF:

0.660

GnomAD4 exome

AF:

0.646

AC:

436795

AN:

675778

Hom.:

144203

AF XY:

0.651

AC XY:

225576

AN XY:

346586

show subpopulations

African (AFR)

AF:

0.474

AC:

7706

AN:

16252

American (AMR)

AF:

0.581

AC:

12518

AN:

21530

Ashkenazi Jewish (ASJ)

AF:

0.701

AC:

10559

AN:

15058

East Asian (EAS)

AF:

0.918

AC:

27402

AN:

29850

South Asian (SAS)

AF:

0.770

AC:

38835

AN:

50420

European-Finnish (FIN)

AF:

0.555

AC:

22646

AN:

40824

Middle Eastern (MID)

AF:

0.780

AC:

1770

AN:

2270

European-Non Finnish (NFE)

AF:

0.629

AC:

294438

AN:

467844

Other (OTH)

AF:

0.659

AC:

20921

AN:

31730

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

7104

14208

21311

28415

35519

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5690

11380

17070

22760

28450

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.601

AC:

91341

AN:

151942

Hom.:

28469

Cov.:

AF XY:

0.607

AC XY:

45086

AN XY:

74278

show subpopulations

African (AFR)

AF:

0.479

AC:

19819

AN:

41414

American (AMR)

AF:

0.631

AC:

9608

AN:

15234

Ashkenazi Jewish (ASJ)

AF:

0.693

AC:

2405

AN:

3468

East Asian (EAS)

AF:

0.937

AC:

4856

AN:

5182

South Asian (SAS)

AF:

0.777

AC:

3747

AN:

4824

European-Finnish (FIN)

AF:

0.548

AC:

5784

AN:

10546

Middle Eastern (MID)

AF:

0.813

AC:

239

AN:

294

European-Non Finnish (NFE)

AF:

0.629

AC:

42739

AN:

67956

Other (OTH)

AF:

0.665

AC:

1404

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1768

3536

5303

7071

8839

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

764

1528

2292

3056

3820

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.625

Hom.:

72818

Bravo

AF:

0.602

Asia WGS

AF:

0.803

AC:

2794

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

2.7

(source)

DANN

Benign

0.24

PhyloP100

-1.5

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over